Supercoil can be partitioned into two parts, twist and writhe, which play distinct roles in genomic processes[1]}. Underwound DNA (with negative twists) can melt the secondary structures of DNA that can attract regulatory proteins[2]}, [3]}, [1]}. In contrast, overwound DNA (with positive twists) can hinder enzymatic activities associated with opening of the DNA duplex, such as in transcription initiation and elongation by RNAP[5]}, [6]}. On the other hand, writhe characterizes spatial crossings of DNA segments[7]}, [8]}, accordingly facilitating distant interactions on DNA[9]}, [10]}, [11]}, [12]}. Writhe can be in a solenoidal or a plectonemic form, or a combination of both. Under an externally stretching force, supercoiled DNA can present a coexistence state of both[13]}, [14]}, [15]}, [16]}, in which the plectonemic coils form the plectonemic (P) phase, while the solenoidal coils are almost straightly stretched, forming the stretched (S) phase[16]}, [18]}.
